Question regarding the UCSC genome browser
Jain, Nitika
I have been trying to find genes for the probe sets in a batch from
UCSC but not able to do so. I could only find the gene for one probeset
at a time. Kindly help me regarding that, as I have a list of more
than 1000 probesets and it is not possible to work on them one at a
time.
Thank you
Dr Nitika Jain
Jonathan Casper
Hello Nitika,
Thank you for your question about finding genes that match your probe sets. I suggest that you start by building a custom track from your probe sets and then use the "intersection" part of the UCSC Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to get the genes that overlap with your probe sets. See http://genome.ucsc.edu/goldenPath/help/customTrack.html for more information about building a custom track, and http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection for more information on using intersections in the Table Browser.
Depending on what gene information you need, the intersection tool might not be enough for your research. If that is the case, the tools at Galaxy (https://usegalaxy.org) can help you to get more specific gene information. The following mailing list questions describe how to use the Table Browser together with the tools at Galaxy to find gene information:
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/LdYxhGwswno/discussion
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/lF0UpVKYi8I/discussion
https://groups.google.com/a/soe.ucsc.edu/d/topic/genome/y7zQDKO-8Hk/discussion
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
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